AU719354B2 - Lipid kinase - Google Patents

Abstract

The invention relates to a novel lipid kinase which is part of the PI3 Kinase family. PI3 Kinases catalyze the addition of phosphate to inositol generating inositol mono, di and triphosphate. Inositol phosphates have been implicated in regulating intracellular signaling cascades resulting in alternations in gene expression which, amongst other effects, can result in cytoskeletal remodeling and modulation of cellular motility. More particularly the invention relates to a novel human PI3 Kinase, p110Delta which interacts with p85, has a broad phosphinositide specificity and is sensitive to the same kinase inhibitors as PI3 Kinase p110A. However, in contrast to previously identified PI3 Kinases which show a ubiquitous pattern of expression, p110Delta is selectively expressed in leucocytes. Importantly, p110Delta shows enhanced expression in most melanomas tested and therefore may play a crucial role in regulating the metastatic property exhibited by melanomas. The identification of agents that enhance or reduce p110Delta activity may therefore prevent cancer metastatis.

Description

Ir WO 97/46688 PCT/GB97/01471 1 LIPID KINASE The invention relates to a novel lipid kinase which is part of the PI3 Kinase (P13K) family and more specifically the invention relates to various aspects of the novel lipid kinase particularly, but not exclusively, to an identification of expression of said kinase with a view to diagnosing or predicting motility or invasion of cells such as metastasis of cancer cells; and also agents for interfering with said expression or inhibiting said kinase with a view to enhancing or reducing or preventing said motility or invasion so as to 1 0 enhance or restrict, respectively the movement of selected cells.

An overview of the PI3 kinase family of enzymes is given in our co-pending Patent Application W093/21328. Briefly, this class of enzymes shows phosphoinositide (hereinafter referred to after as PI) 3-kinase activity.

Following major advances in our knowledge of cell signal transduction and 1 5 cell second messenger systems it is known that the PI3Ks have a major role to play in regulating cell function. Indeed, it is known that PI3Ks are members of a growing number of potential signalling proteins which associate with protein-tyrosine kinases activated either by ligand stimulation or as a consequence of cell transformation. Once thus associated they provide an important complex in the cell signalling pathway and thus direct events towards a given conclusion.

PI3 kinases catalyse the addition of phosphate to the 3'-OH position of the inositol ring of inositol lipids generating phosphatidyl inositol monophosphate, phosphatidyl inositol diphosphate and phosphatidyl inositol triphosphate (Whitman et al, 1988, Stephens et al 1989 and 1991). A family if 'h WO 97/46688 PCT/GB97/01471 2 of PI3 kinase enzymes has now been identified in organisms as diverse as plants, slime molds, yeast, fruit flies and mammals (Zvelebil et al, 1996).

It is conceivable that different PI3 kinases are responsible for the generation of the different 3'-phosphorylated inositol lipids in vivo. Three classes of PI3 kinase can be discriminated on the basis of their in vitro lipid substrates specificity. Enzymes of a first class have a broad substrate specificity and phosphorylate PtdIns, PtdIns(4)P and PtdIns(4,5)P2. Class I PI3 kinases include mammalian pll0a, pllOP and p11Oy (Hiles et al, 1192; Hu et al, 1993; Stephens et al, 1994; Stoyanov et al, 1995).

Pll0a and p110p are closely related PI3 kinases which interact with adaptor proteins and with GTP-bound Ras.

Two 85 kDa subunits, p85a and p85 have been cloned (Otsu et al, 1992).

These molecules contain an N-terminal src homology-3 (SH3) domain, a breakpoint cluster (bcr) homology region flanked by two proline-rich regions 1 5 and two src homology-2 (SH2) domains. Shortened p85 proteins, generated by alternative splicing from the p85a gene or encoded by genes different from those of p85a/, all lack the SH3 domain and the bcr region, which seem to be replaced by a unique short N-terminus (Pons et al, 1995; Inukai et al, 1996; Antonetti et al, 1996). The SH2 domains, present in all molecules, provide the heterodimeric p85/p110 PI3Ks with the capacity to interact with phosphorylated tyrosine residues on a variety of receptors and other cellular proteins. In contrast to pll0a and P, p110y does not interact with p85 but instead associates with a pl01 adaptor protein (Stephens et al, 1996). P110y activity is stimulated by G-protein subunits.

WO 97/46688 PCT/GB97/01471 3 PI3Ks of a second class contains enzymes which, at least in vitro, phosphorylate Ptdlns and PtdIns(4)P but not Ptdlns(4, 5)P 2 (MacDougall et al, 1995; Virbasius et al, 1996, Molz et al, 1996). These PI3Ks all contain a C2 domain at their C-terminus. The in vivo role of these class II PI3Ks is unknown.

A third class of PI3K has a substrate specificity restricted to PtdIns. These PI3Ks are homologous to yeast Vps34p which is involved in trafficking of newly formed proteins from the Golgi apparatus to the vacuole in yeast, the equivalent of the mammalian lysosome (Stack et al, 1995). Both yeast and mammalian Vps34p occur in a complex with Vpsl5p, a 150 kDa protein serine/threonine kinase (Stack et al, 1995; Volinia et al, 1995; Panaretou et al, submitted for publication).

PtdIns(3)P is constitutively present in cells and its levels are largely unaltered upon extracellular stimulation. In contrast, Ptdlns(3, 4)P 2 and Ptdlns(3, 4, 1 5 5)P 3 are almost absent in quiescent cells but are produced rapidly upon stimulation by a variety of growth factors, suggesting a likely function as second messengers (Stephens et al, 1993). The role of PI3Ks and their phosphorylated lipids in cellular physiology is just beginning to be understood. These lipids may fulfill a dual role: apart from exerting physical, charge-mediated effects on the curvature of the lipid bilayer, they also have the capacity to interact with specific binding proteins and modulate their localisation and/or activity. Amongst the potential targets for these lipids are protein kinases such as protein kinase C isoforms, protein kinase N/Rhoactivated kinases and Akt/RAC/protein kinase B (Toker et al, 1994; Palmer et al, 1995; Burgering and Coffer, 1995; Franke et al, 1995; James et al, 1996; Klippel et al, 1996). Akt/RAC/protein kinase B is likely to be WO 97/46688 PCT/GB97/01471 4 upstream of targets such as p70 S6 kinase and glycogen synthase kinase-3 (Chung et al, 1994; Cross et al, 1995). PI3Ks also affect the activity of small GTP-binding proteins such as Rac and Rab5, possibly by regulating nucleotide exchange (Hawkins et al, 1995; Li et al, 1996). Ultimately, the combination of these actions can result in cytoskeletal rearrangements, DNA synthesis/mitogenesis, cell survival and differentiation (Vanhaesebroeck et al, 1996).

We describe herein a mammalian novel Class I PI3 Kinase which we have termed p1106. This novel PI3 Kinase typifies the Class I PI3 Kinase family in that it binds p85 a, p85 P and p 8 5y. In addition, it also binds GTP-ras but, like pll0a, shows no binding of rho and rac. It also shares the same GTPbroad phosphoinositide lipid substrate specificity of pll0a and p110P, and it also shows protein kinase activity and has a similar drug sensitivity to pllOa.

1 5 However, it is characterised by its selective tissue distribution. In contrast to pllOa and pllO which seem to be ubiquitously expressed, p1106 expression is particularly high in white blood cell populations i.e. spleen, thymus and especially peripheral blood leucocytes. In addition to this observation we have also found that p1108 is expressed in most melanomas, but not in any melanocytes, the normal cell counterpart of melanomas. Given the natural distribution of p1106 in tissues which are known to exhibit motility or invasion and also the expression of p1106 in cancer cells we consider that p110 6 has a role to play in cell motility or invasion and thus the expression of this lipid kinase in cancer cells can explain the metastatic behaviour of cancer cells.

a h WO 97/46688 PCT/GB97/01471 A further novel feature of p1106 is its ability to autophosphorylate in a Mn 2 dependent manner. Indeed, we have shown that autophosphorylation tends to hinder the lipid kinase activity of the protein. In addition, p1106 contains distinct potential protein:protein interaction modules including a proline-rich region (see Figure 1, position 292-311, wherein 8 out of 20 amino acids are proline) and a basic region leucine zipper (bZIP) like domain (Ing et al., 1994 and Hirai et al., 1996). Such biochemical and structural differences between PI3 kinases indicate that they may fulfill distinct functional roles and/or be differentially regulated in vivo.

We disclose herein a nucleic acid molecule, of human origin, and corresponding amino acid sequence data relating to p1106. Using this information it is possible to determine the expression of p1106 in various tissue types and in particular to determine the expression of same in cancer tissue with a view to diagnosing the motility or invasiveness of such tissue 1 5 and thus predicting the potential for secondary tumours occurring. Moreover, it will also be possible to provide agents which impair the expression of p1108 or alternatively interfere with the functioning of same. For example, having regard to the sequence data provided herein it is possible to provide antisense material which prevents the expression of p 110.

As mentioned above, the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a PI3K8 protein, to decrease transcription and/or translation of PI3K6 genes. This is desirable in virtually any medical condition wherein a reduction in PI3K6 gene product expression is desirable, including to reduce any aspect of a tumor cell phenotype attributable to PI3K8 gene expression. Antisense molecules, in this manner, can be used to slow down or arrest such aspects of a tumor cell h WO 97/46688 PCT/GB97/01471 6 phenotype.

As used herein, the term "antisense oligonucleotide" or "antisense" describes an oligoneucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and thereby, inhibits the transcription of that gene and/or the translation of that mRNA. The antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene. Those skilled in the 1 0 art will recognize that the exact length of the antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence of the target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with 1 5 the target under physiological conditions, to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. Based upon the DNA sequence presented in Figure 9 or upon allelic or homologous genomic and/or DNA sequences, one of skill in the art can easily choose and synthesize any of a number of appropriate antisense molecules for use in accordance with the present invention. In order to be sufficiently selective and potent for inhibition, such antisense oligonucleotides should comprise at least 7 (Wagner et al., Nature Biotechnology 14:840-844, 1996) and. more preferably, at least consecutive bases which are complementary to the target. Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases. Although oligonucelotides may be chosen which are antisense to any region of the gene or mRNA transcripts, in preferred embodiments the WO 97/46688 PCT/GB97/01471 7 antisense oligonucleotides correspond to N-terminal or 5' upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3'-untranslated regions may be targeted. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, Sainio et al., Cell Mol. Neurobiol. 14(5):439-457. 1994) and at which proteins are not expected to bind. Finally, although Figure 9 discloses cDNA sequence, one of ordinary skill in the art may easily derive the genomic DNA corresponding to the cDNA of Figure 9. Thus, the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to Figure 9. Similarly, antisense to allelic or homologous DNAs and genomic DNAs are enabled without undue experimentation.

In one set of embodiments, the antisense oligonucleotides of the invention 1 5 may be composed of "natural" deoxyribonucleotides, ribonucleotides, or any combination thereof. That is, the 5' end of one native nucleotide and the 3' end of another native nucleotide may be covalently linked, as in natural systems, via a phosphodiester internucleoside linkage. These oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.

In preferred embodiments, however, the antisense oligonucleotides of the invention also may include "modified" oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness.

WO 97/46688 PCT/GB97/01471 8 The term "modified oligonucleotide" as used herein describes an oligonucleotide in which at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide) and/or a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide.

Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, phosphate triesters, 1 0 acetamidates, peptides, and carboxymethyl esters.

The term "modified oligonucleotide" also encompasses oligonucleotides with a covalently modified base and/or sugar. For example, modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a 1 5 hydroxyl group at the 3' position and other than a phosphate group at the position. Thus modified oligonucleotides may include a 2'-0-alkylated ribose group. In addition, modified oligonucleotides may include sugars such as arabinose instead of ribose. Modified oligonucleotides also can include base analogs such as C-5 propyne modified bases (Wagner et al., Nature Biotechnology 14:840-844, 1996). The present invention, thus, contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding PI3K6 proteins, together with pharmaceutically acceptable carriers.

Antisense oligonucleotides may be administered as part of a pharmaceutical composition. Such a pharmaceutical composition may include the antisense WO 97/46688 PCT/GB97/01471 9 oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art. The compositions should be sterile and contain a therapeutically effective amount of the antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. The term "physiologically acceptable" refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration. Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art.

It is therefore an object of the invention to identify a novel PI3 Kinase and so provide means for predicting the likely motility or invasiveness of cells.

It is a yet further object of the invention to provide agents that enhance or reduce or prevent the expression of p1106 and/or agents which interfere with the functioning of p1106, with a view to enhancing or hindering or preventing, respectively, the motility or invasiveness of cells.

According to a first aspect of the invention there is therefore provided an isolated autophosphorylating polypeptide which possesses PI3 kinase activity.

Ideally said polypeptide is derived from white blood cells and is typically expressed in melanomas, more ideally still said polypeptide is of human origin.

WO 97/46688 PCT/GB97/01471 Moreover, the polypeptide is capable of association with p85 subunits of mammalian PI3 Kinases ideally to produce active complexes.

More preferably still the polypeptide has the amino acid sequence shown in Fig. 1A or a sequence homologous 'thereto which is in particularly characterised by a proline rich domain.

Reference herein to the term homologous is intended to cover material of a similar nature or of common descent or pocessing those features, as herein described, that characterise the protein, or material, whose corresponding nucleic acid molecule hybridises, such as under stringent conditions, to the 1 0 nucleic acid molecule shown in Figure 9. Typical hybridisation conditions would include 50% formamide, 5 X SSPE, 5 X Denhardts solution, 0.2% SDS, 200 lig/ml denatured sonicated herring sperm DNA and 200 tg/ml yeast RNA at a temperature of 60° C, (conditions described in the published patent specification WO 93/21328).

Ideally the polypeptide is produced using recombinant technology and is typically of human origin.

According to a further aspect of the invention there is provided an antibody to at least a part of the polypeptide of the invention, which antibody may be polyclonal or monoclonal.

According to a further aspect of the invention there is provided the whole or a part of the nucleic acid molecule shown in Fig. 9 which molecule encodes an autophosphorylating polypeptide having PI3 Kinase activity.

WO 97/46688 PCT/GB97/01471 11 In the instance where said part of said molecule is provided, the part will be selected having regard to its purpose, for example it may be desirable to select a part having kinase activity for subsequent use or another part which is most suitable for antibody production.

According to a further aspect of the invention there is provided a nucleic acid molecule construct comprising a whole or a part of the nucleic acid molecule of the invention wherein the latter nucleic acid molecule is under the control of a control sequence and in appropriate reading frame so as to ensure expression of the corresponding protein.

According to a yet further aspect of the invention there is provided host cells which have been transformed, ideally using the construct of the invention, so as to include a whole or a part of the nucleic acid molecule shown in Fig.

9 so as to permit expression of a whole, or a significant part, of the corresponding polypeptide.

Ideally these host cells are eukaryotic cells for example, insect cells such as cells from the species Spodopterafrugiperda using the baculovirus expression system. This expression system is favoured in the instance where post translation modification is required. If such modification is not required a prokaryotic system may be used.

According to a further aspect of the invention there is provided a method for diagnosing the motility of cells comprising examining a sample of said cells for the expression of the polypeptide of the invention.

Ideally, investigations are undertaken in order to establish whether mRNA I l WO 97/46688 PCT/GB97/01471 12 corresponding to the polypeptide of the invention is expressed in said cells, for e.g. by using PCR techniques or Northern Blot analysis. Alternatively, any other conventional technique may be undertaken in order to identify said expression.

According to a yet further aspect of the invention there is provided a method for identifying antagonists effective at blocking the activity of the polypeptide of the invention which comprises screening candidate molecules for such activity using the polypeptide, or fragments thereof the invention.

Ideally, screening may involve artificial techniques such as computer-aided 1 0 techniques or conventional laboratory techniques.

Ideally, the above method is undertaken by exposing cells known to express the polypeptide of the invention, either naturally or by virtue of transfection, to the appropriate antagonist and then monitoring the motility of same.

Alternatively, the method of the invention may involve competitive binding 1 5 assays in order to identify agents that selectively and ideally irreversibly bind to the polypeptide of the invention.

According to a yet further aspect of the invention there is provided a pharmaceutical or veterinary composition comprising an agent effective at enhancing or blocking the activity or expression of the polypeptide of the invention which has been formulated for pharmaceutical or veterinary use and which optionally also includes a dilutant, carrier or excipient and/or is in unit dosage form.

WO 97/46688 PCT/GB97/01471 13 According to a yet further aspect of the invention there is provided a method for controlling the motility of cells comprising exposing a population of said cells to either an agonist or antagonist or the polypeptide of the invention or to antisense material as hereindescribed.

Alternatively, in the aforementioned method said cells may be exposed alternatively or additionally, to the polypeptide of the invention with a view to increasing the effective levels of said polypeptide and so enhancing cell motility.

The aforementioned method may be undertaken either in vivo or in vitro.

1 0 According to a yet further aspect of the invention there is provided use of an agent effective at blocking the activity of the polypeptide of the invention for controlling cell motility.

According to a yet further aspect of the invention there is provided use of the polypeptide of the invention for enhancing cell motility.

1 5 According to a yet further aspect of the invention there is provided antisense oligonucleotides ideally modified as hereindescribed, for hybridizing to the nucleic acid of the invention.

An embodiment of the invention will now be described by way of example only with reference to the following figures, materials and methods wherein: Fig. 1(A) shows translated amino acid sequence of human p1106 cDNA.

The proline-rich region and the bZIP-like domain are indicated by open and WO 97/46688 PCT/GB97/01471 14 shaded box, respectively. Dotplot comparison of the full length amino acid sequence of p110 8 with that of pll0a and pllO0. Non-conserved sequence motifs are underlined. Dotplot comparisons were performed using the COMPARE program (UWGCG package: Devereux et al, 1984). (C) Comparison of the p1108 amino acid sequence flanking HR3 with respective homologous regions of p110 a and p11013. Amino acid numbering is that of p1106. Proline-rich region: critical prolines enabling the formation of a lefthanded polyproline type-II helix in p110 8 are indicated with an asterisk.

bZIP region: conserved L/V/I residues of the leucine-zipper region are 1 0 indicated with arrowheads.

Fig. 2. Interaction of pl10 8 with p85 and Ras Insect cells were infected with recombinant baculovirus encoding GST-p 1108, alone or in combination with viruses encoding either p85a, P or y. After 2 days, GST-p1108 was affinity-purified from the cell lysates using glutathione-sepharose, washed, and analysed by SDS-PAGE and Coomassie staining. P1108 was immunoprecipitated from 500 ptg human neutrophil cytosol and probed for the presence of different p85 isoforms by Western blotting. rec recombinant purified from Sf9 cells. GST-pl 10a/85ac and GST-pl108/85a (0.25 g/g) were incubated with the indicated amount (in tug) of GTP- or GDPloaded V12-Ras, washed and probed for the presence of Ras by Western blotting as described (Rodriguez-Viciana et al, 1994, 1996).

Fig. 3. In vitro lipid substrate specificity of p1106. GST-pl 106/p85a was used in a lipid kinase assay using the indicated substrates in the presence of Mg 2 Equal cpm were spotted at the origin. HPLC analysis of the Ptdlns phosphorylation product generated by GST-p1108/p85 a. Elution times of the deacylated product of p1106 (solid line) and WO 97/46688 PCT/GB97/01471 glycerophosphoinositol-3P and glycerophosphoinositol-4P standards (dotted lines) are shown. The positions of the AMP and ADP controls are indicated by arrows.

Fig. 4. Protein kinase activity of pl108. GST-pllOa or GST-pll06, in complex with the indicated p85 subunits, were subjected to an in vitro protein kinase reaction in the presence of Mn 2 and further analysed by SDS- PAGE, Coomassie staining and autoradiography, Untagged pl10a and p1108 [wild-type (WT) or kinase defective mutants (pll0a-R916P and pl108-R894P)], in complex with p85a or P on PDGF-receptor 1 0 phosphopeptide beads, were subjected to an in vitro kinase reaction and further analysed as described under Open and closed arrowheads point to p110 and p85 proteins, respectively. Right panel in phosphoamino acid analysis of p85a and p1108.

Fig. 5. Sensitivity of p1108 lipid kinase activity to drugs. Inhibition of 1 5 p1108/p85a (closed circles) and p110a/p85a (open circles) is normalised to activity in the absence of the drug wortmannin. These data points are the mean of 3 experiments.

Fig. 6. Northern blot analysis of expression of pl10a, pllO0 and p1108.

Fig. 7. Analysis of pll0a and p 1 106 protein expression. 100/g of total cell lysate was loaded per lane. Platelets were lysed in either lysis buffer as described under Materials and Methods, or in Laemmli gel loading buffer containing 2-mercaptoethanol. PMBC, peripheral blood mononuclear cells; PBL, peripheral blood lymphocytes.

WO 97/46688 PCT/GB97/01471 16 Fig. 8. Involvement of pllOa and p110 8 in cytokine signalling. Ba/F3 (A) and MC/9 cell lines were stimulated with the indicated cytokines.

Samples from control untreated cells are labelled Con. Total cell lysates, and pllOc and pl108 IPs were separated by SDS-PAGE to prepare duplicate blots, the references for which were p 1 106/85a (panels a, b and d) or p110a/85a (panels c and Immunoblotting of native blots were performed with 4G10 (anti-PTyr, panels a) and anti-pllOa (panels Blots were subsequently stripped and reprobed with anti-SHP2. panel anti-kit (B, panel anti-pll06 (panels d) and anti-p85 antibodies (panels The 1 0 arrowheads indicate the positions of p170 (IRS-2), p100 and p70 (SHP2) (A, panel and of p150 (c-kit) and pl00 panel b).

Fig. 9. The complete human cDNA sequence of p1106.

Fig. 10. Represents immunofluorescence images of murine macrophages microinjected with affinity purified antibodies to p1106. The macrophage 1 5 cytoskeletons are imaged with phalloidin conjugated rhodamine.

MATERIALS AND METHODS Cloning of p1106 Details of the isolation of partial PI3 kinase cDNA clones via RT-PCR based on homologous regions between bovine p 10a and S. cerevisiae Vps34p have been described (Volinia et al., 1995: MacDougall et al., 1996). This approach yielded from the MOLT4 T cell line a partial p1106 cDNA fragment which was then used to screen an oligo(dT)-primed U937 cDNA library (Volinia et al., 1995). Complementary DNA was EcoRI-XhoI cloned WO 97/46688 PCT/GB97/01471 17 in Lambda ZAPII vector digested with EcoRI-XhoI (Stratagene). Out of 4 million clones screened, 6 primary positive plaques were found, 3 of which remained positive during two further rounds of screening. The cDNA inserts in pBluescript were prepared by in vivo excision according to the manufacturer's (Stratagene) instructions. Three representative pBluescript clones (05.1, 09. and 011.1) were characterised by restriction mapping and PCR, and found to contain inserts with sizes ranging from 4.4 kb to 5.0 kb 09.1). Clone 09.1 was used for detailed characterisation. Restriction mapping of its insert revealed the absence of an internal XhoI site, and the 1 0 presence of 2 internal EcoRI sites, respectively 223 and 3862 nucleotides 3' from the EcoRI cDNA insertion site (nucleotide 1 underlined nucleotide of Figure Consequently, combined EcoRI and XhoI digest divided the 09.1 insert in 3 fragments, further indicated as EcoRI fragment I (nucleotide 1- 222), EcoRI fragment II (nucleotide 223-3861) and EcoRI-XhoI fragment III 1 5 (nucleotide 3862-5000 approximately). Both strands of fragments I and II were sequenced using the Taq DyeDeoxy Terminator Cycle sequencing system (ABI) and the complete cDNA sequence is shown in Fig. 9. An open reading frame spanning nucleotides 195 to 3330 of the 09.1 insert was found.

An in frame stop codon precedes the potential start codon, which lies in a favourable context for translation initiation (Kozak, 1991). This results in 196 nucleotides of 5' untranslated region (UT) and approximately 2.2 kb 3' UT. In the sequenced 5' end of 05., 09.1 and clones, 2 different but related 5' untranslated regions were found indicative for the existence of at least 2 slightly different messenger RNAs.

Construction of expression vectors for p1108 Insect cell transfer vectors used were pVL1393 (for untagged p1106; WO 97/46688 PCT/GB97/01471 18 InVitrogen) and pAcG3X (for GST-p1108; Davies et al., 1993). The coding region for p1108 was subcloned in these vectors in two steps. First, the expression vectors were engineered, via linker insertion at the multicloning site, to contain part of the sequence of EcoRI fragment I of p1108, spanning the start codon (at nucleotide 197; see above) to the second EcoRI site (nucleotide 223; see above). In the latter EcoRI site, EcoRI fragment II of p1108 was subcloned, followed by selection for clones with correctly orientated inserts. The first step for the insect cell vectors was BamHI-EcoRI cleavage followed by insertion of the following linker (linker I): GATCCCCACCATGCCCCCTGGGGTGGACTGCCCCATGG (sense: (antisense: 5'-3')AATTCCATGGGGCAGTCCACCCCAGGGGGCATGGTGGG This linker contains the ATG with an optimal Kozak consensus sequence (Kozak, 1991). Further derivatives of p1106 were made by PCR using Vent DNA polymerase (New England Biolabs). P1106 EcoRI fragment II, 1 5 subcloned in pBluescript-SK (further indicated as pBluescript-p1108-EcoII) was hereby used as a template. In these PCR reactions, the 3'-untranslated region of the EcoRI fragment II insert was removed. Oligonucleotides used to create the mutation R894P were as follows: sense mutagenic oligonucleotide PRIMER 1 (mutagenic residue underlined)

ACATCATGATCCG,

Anti-sense PRIMER 2 WO 97/46688 PCT/GB97/01471 19

TGTGGGCC.

A parallel PCR was performed using primer 2, and a sense primer (PRIMER 3 GTGTGGCCACATATGTGCTGGGCATTGGCG) leaving the wild type p1108 sequence intact. All PCR products were cleaved with NdeI and XhoI, subcloned into NdeI-XhoI-opened pBluescript-pll06-EcoII and sequenced. Correct clones were then transferred as an EcoRI cassette into EcoRI-opened pVL1393 containing linker I followed by selection for clones with correctly orientated insert.

Expression of p1106 in insect cells 1 0 Plasmid DNA was cotransfected with BaculoGold DNA (Pharmingen, San Diego, CA) using Lipofectin reagent (Gibco). Recombinant plaques were isolated and characterised by established methods (Summers and Smith, 1987).

Cell Culture 1 5 Cells were cultured in a humidified 5% CO 2 incubator in RPMI 1640 medium supplemented with 10% fetal bovine serum, 20 yM 2-mercaptoethanol, 100 units/ml penicillin/streptomycin and 2 mM glutamine. Ba/F3 is a murine IL3-dependent pre-B cell line (Palacios and Steinmetz, 1985) and MC/9 is a murine IL3-dependent mast cell line (Nabel et al., 1981). Both Ba/F3 and MC/9 were maintained in 10% conditioned medium derived from WEHI3B, as the source of murine IL3. FDMAC11/4.6 (FD-6) myeloid progenitor cells are an indigenous variant of FDMAC 11 which will grow in response to IL4, as well as IL3, GM-CSF and CSF-1 (Welham et al., 1994a).

WO 97/46688 PCT/GB97/01471 These cells were maintained in 3% IL4-conditioned medium derived from the AgX63/OMIL4 cells (Karasuyama and Melchers, 1988).

Lipid Kinase assay Lipid kinase activity was performed essentially as described by Whitman et al. (1985). Lipid kinase assay buffer was 20 mM Tris HCI pH 7.4, 100 mM NaCl and 0.5 mM EGTA. Lipids were purchased from Sigma. The final concentration of ATP and Mg 2 in the assay were routinely 0.5 and 3.5 mM, respectively, while lipids were used at 0.2-0.4 mM concentration. Unless otherwise indicated, kinase reaction was for 10 min at 37 C. The solvent for 1 0 TLC separation of reaction products was propan-l-ol/2 M acetic acid/5 M

H

3

PO

4 (65:35:1). Assays of drug effects on the kinase were performed using Ptdlns as substrate in the presence of 40 iM ATP (final) for 10 min at all tubes contained 1% DMSO. Activity was quantified by phosphorimager (Molecular Dynamics) analysis of TLC-separated lipid products.

1 5 HPLC analysis 3 2 P]-PtdIns3P, prepared by phosphorylating PtdIns with recombinant p 110a, and 32 P]-PtdIns4P, generated by converting PtdIns with A431 membranes in the presence of 0.5% NP-40, were used as standards.

Glycerophosphoinositols, generated by deacylation of lipids with methylamine (Clarke and Dawson, 1981), were separated by anion exchange HPLC on a PartisphereSAX column (Whatman International) using a linear gradient of 1 M (NH 4 2 HP0 4 against water (0-25% B; 60 min) at Iml/min. Radioactive peaks were detected by an on-line detector (Reeve Analytical, Glasgow).

WO 97/46688 PCT/GB97/01471 21 ADP and ATP nucleotide standards, added as internal controls to ensure consistency between runs, were detected by absorbance at 254nm.

In vitro protein phosphorylation assay and effect on lipid kinase activity Precipitated proteins were incubated for 30 min at 37 C in protein kinase assay buffer (20 mM Tris.HC1 (pH 100 mM NaCI, 0.5 mM EGTA, pM ATP and 1 mM MnC 2 .4H0, 5-10 /Ci[ y- 32 P]ATP/ml). The reaction was stopped by addition of SDS-PAGE sample buffer, and the reaction products analysed by SDS-PAGE and autoradiography. Phosphoamino acid analysis was performed on a Hunter thin layer electrophoresis system (CBS Scientific Co, Del Mar, CA) as described (Jelinek and Weber, 1993).

Interaction of small GTP-binding proteins with PI-3K in vitro Binding of ras, rac and rho to GST-PI3K was performed as described (Rodriguez-Viciana et al., 1995, 1996).

Antibodies, immunoprecipitations and immunoblotting 1 5 Monoclonal antibodies to bovine p85a (Ul, U13), and p85 3 (T15) have been described (End et al., Reif et al., 1993). A monoclonal antibody (12) against bovine p85y was developed in our laboratory. Rabbit polyclonal antiserum against GST-human p85a (AA 5-321) was kindly provided by Dr. P.

Shepherd, University College London. Rabbit polyclonal antisera were raised against a C-terminal peptide of p1106 (C)KVNWLAHNVSKDNRQ 044 and against an N-terminal peptide of human pll0a (CGG)SVTQEAEEREEFFDETRRs. To raise antibodies directed against the WO 97/46688 PCT/GB97/01471 22 phosphorylated form of p1108, the peptide sequence 1044 was phosphorylated at the serine residue during peptide synthesis. An antiserum to the C-terminus of human pll0a (KMDWIFHTIKQHALN) was kindly provided by Dr. Roya Hooshmand-Rad (Ludwig Institute for Cancer Research, Uppsala, Sweden). Antibodies were affinity-purified on peptides coupled to Actigel (Sterogene Bioseparations, Arcadia, CA) or to AF-Amino ToyoPearl TSK gel (Tosho Co, Japan). Antibodies were found to be specific for the PI3K to which they were directed (tested against the following panel of PI-3K, expressed in Sf9 cells: bovine pl10a, human p1100 Panaretou 1 0 and unpublished results), human p1lOy (Stoyanov et al., 1995), p1108, PI-specific 3 -kinase (Volinia et al 1995). Peripheral blood cells were purified over a ficoll gradient (Lymphoprep; Nycomed, Oslo, Norway).

Neutrophil cytosol was prepared by sonication as described (Wientjes et al., 1993). Lysis buffer was 1% Triton-X100, 150 mM NaC1, 1 mM EDTA, 1 mM NaF, 1 mM NaVO 3 1 mM DTT, 1 mM PMSF, 0.27 TIU/ml aprotinin and 10 /M leupeptin. In some experiments, 1mM disopropylfluorophosphate and 27 mM Na-p-tosyl-L-lysine chloromethyl ketone (hydrochloride) were added. Lysis buffer used for cytokine experiments was 50 mM Tris.HC1, pH 10% glycerol, 1% NP-40, 150 mM NaCI, 100 ,4M sodium molybdate, 500 kiM sodium fluoride, 100 uM sodium orthovanadate, 1 mM EDTA, 40 Mg/ml PMSF, 10 jg/ml aprotinin, 10 ,ug/ml leupeptin, 0.7 jig/ml pepstatin, 1 mM DIFP, 1 mM TLCK). Cytokine-stimulated cells were pelleted and lysed at 2 x 10 7 cells/ml as described (Welham and Schrader, 1992) with the exception that lysates were clarified for 5 min in a microfuge ay 40C prior to further analyses. Immunoprecipitations were carried out as described (Welham et al., 1994a) PDGF-receptor peptide (YpVPMLG) was coupled to Actigel according to the manufacturer's instructions. C-terminal antiserum to p1108 was used for both immunoprecipitations and WO 97/46688 PCT/GB97/01471 23 immunoblotting. For pll0a, the C- and N-terminal antisera were used for immunoprecipitations and Westerns blot analysis, respectively.

SDS-PAGE and immunoblotting were carried out as described (Laemmli, 1970; Welham and Schrader, 1992; Welham et al., 1994a). Antibodies were used at the following concentrations for immunoblotting: 4G10, antiphosphotyrosine monoclonal antibody at 0.1 mg/ml; anti-pllOa and p1108 at 0.25 pg/ml; anti-p85 at 1:4000; anti-c-kit (Santa Cruz Biotechnology, sc-168) at 0.4 pg/ml, anti-SHP (Santa Cruz Biotechnology, sc-280) at 0.1 gg/ml and anti-IRS-2 (gift of Dr. M. White, Joslin Diabetes 1 0 Center, Boston, MA) at 1:1000.

Both goat and anti-mouse and goat anti-rabbit horseradish peroxidaseconjugated antibodies (Dako, Denmark) were used at a concentration of 0.05 /tg/ml. Immunoblots were developed using the ECL system (Amersham).

Blots were stripped and reprobed as previously described (Welham et al., 1994a).

Injection of CSF-1 Stimulated Mouse Macrophages with Antibodies to p1106 and pll0a The murine macrophage cell-line, BAC1, was used in antibody micro injection experiments. The peptide polyclonal antibodies to p1106 were directed to either the C-terminal peptide 1044, (described p17 Materials and Methods), or to the peptide sequence (C)R222KKATVFRQPLVEQPED 23 8.

Polyclonal sera were affinity purified before micro injection and were used at a concentration of 0.5-5 mg/ml. A control peptide polyclonal antisera to human Pll0a is as described on p17 of Materials and Methods. Before WO 97/46688 PCT/GB97/01471 24 micro injection, Bad cells were starved of Colony Stimulating Factor 1 (CSF1) for 24 hours. Antibodies were then injected into CSF1 starved cells and exposed to CSF1 for 10-15 minutes before visualisation of the cytoskeleton of micro injected Bad cells with phalloidin conjugated rhodamine, (preparation and visualisation of cells is as described in Allen et al 1997).

Cell stimulations Stimulation of cells with different growth factors was carried out as described (Welham and Schrader, 1992) with the exception that cells were resuspended at 2x10 7 /ml in serum-free RPMI prior to stimulations. Chemically synthesized murine IL3 and IL4 were kindly provided by Dr. Ian Clark-Lewis (University of British Columbia, Vancouver). Recombinant murine SCF was purchased from R&D Systems Europe (Abingdon, Oxon). The concentration of growth factors and duration of stimulation (2 minutes for SCF; 10 minutes 1 5 for IL3 and IL4) had been previously optimised to obtain maximal levels of tyrosine phosphorylation of receptors and cellular substrates. These were as follows, IL3 at 10 ig/ml (Welham and Schrader, 1992), IL4 at 10 g/ml (Welham et al., 1994a) and SCF 50 ng/ml unpublished observations).

Northern blot analysis Northern blots of human polyA+ RNA (Clontech) were hybridized with random prime-labelled EcoRI fragment II of pBluescript clone 09,. Stripping and reprobing using the following subsequent probes was then performed: internal EcoRI-XhoI 2.1 kb fragment from human pll0a (Volinia et al., WO 97/46688 PCT/GB97/01471 1994) and EcoRI-XhoI 5 kb cDNA of human pl10P Panaretou; unpublished results).

Using the above described materials and methods we were able to elucidate data which describes the novel lipid kinase and in particular a PI3 Kinase which we have termed p1106. Data relating to this kinase will now be described with a view to comparing p110 6 with other members of the PI3 Kinase group so as to compare and contrast their respective characteristics.

RESULTS

Cloning of p1106 Degenerate primers based on conserved amino acid sequences (GDDLRQD and FHI/ADFG) in the kinase domain of bovine pll0a and S. cerevisiae Vps34p were used in RT-PCR reactions with mRNA from the human MOLT4 T cell leukaemia. A partial cDNA, homologous but different from other known human PI3K, was obtained. This PCR fragment was used as a 1 5 probe to screen a U937 monocyte library, and to isolate the corresponding full length clone (for details, see Materials and Methods and Fig. 9).

Sequence analysis revealed a potential open reading frame, preceded by an in-frame stop codon. The potential start codon was also found to lie in a favourable context for translation initiation (Kozak, 1991). This open reading frame of 3135 nucleotides predicts a protein of 1044 amino acids with a calculated molecular mass of 119,471 daltons (Fig. 1A). Comparison of the amino acid sequence with other PI3K showed that this protein is most WO 97/46688 PCT/GB97/01471 26 closely related to human pll0P (58% overall identity; Hu et al., 1993), and more distantly to human pll0a (41% identity; Volinia et al., 1994), human G-protein regulated p1lOy (35% identity; Stoyanov et al., 1995) and the human vps34p analogue (28% identity; Volinia et al., 1995). The new PI3K described here will be further indicated as p1106.

Dot plot comparison at high stringency (Fig. 1B) shows that p110a, and 8 are very homologous in the p85-binding region (AA 20-140 of pllOa; Dhand et al., 1994) as well as in the C-terminal PI-kinase (PIK) domain (HR2) and catalytic core (AA 529-end of p110a, Zvelebil et al., 1996). An 1 0 additional region of high sequence homology, spanning AA 370-470 of p 1 108, was found in between the p85 binding site and HR2. This region contains the so-called HR3 signature (WxxxLxxxIxIxDLPR/KxAxL) which is conserved in all p85-binding PI3Ks and in p11Oy. The most N-terminal area of sequence difference between pll10a and p1100 6 overlaps with the 1 5 region defined in pll0a as being sufficient for Ras binding (AA 133-314 in pll0a; Rodriguez-Viciana et al., 1996). Two additional structural motifs were identified in p1106. The first is a proline-rich region (Figure 1B, C) for which molecular modelling indicates that it can form a left-handed, polyproline type-II helix with the potential to interact with SH3 domains (data not shown). In the corresponding region, pll110 and pl10 lack crucial prolines to allow a similar fold. The second motif is a basic-region, leucinezipper (bZIP)-like domain, immediately C-terminal of HR3 (Figure 1B, C).

A bZIP region is present in both p 1 108 and p1lOP (and also in the Drosophila p110 (Leevers et al., 1997)), whereas the basic component of this domain is less prominent in p 110a (Figure 1C). Modelling of the p 1106 ZIP region shows that its arrangement of L/V/I residues easily accommodates the formation of a helix structure which can form a coiled-coil dimeric protein WO 97/46688 PCT/GB97/01471 27 zipper complex (data not shown).

pl1 0 6 binds the p85 adaptor and Ras proteins In order to verify the prediction from amino acid sequence comparison that p1106 might bind p85 subunits, p1108 was expressed in insect cells as a glutathione-S-transferase (GST)-fusion protein, together with recombinant baculoviruses encoding p85a, p85 P or p85y (the latter is a 55 kDa bovine isoform homologous to p55 P IK p55a and p85/AS53 (Pons et al., 1995; Inukai et al., 1996; Antonetti et al., 1996)). As is clear from Figure 2A all adaptor subtypes efficiently co-purified with GST-pll0 from co- 1 0 infected cells.

The question of whether different class I p110 catalytic subunits show binding preference for different p85 adaptor proteins in vivo has not been previously addressed. Using antiserum specific for p 1106, we found that both and p85p were present in p1106 immunoprecipitates from different 1 5 white blood cells (Figure 2B shows the data for human neutrophils; note that is not expressed in leukocytes). Similar results were obtained for pll0a (data not shown). In these immune complexes, a 45 kDa protein reactive with p85 a antibodies was also observed (Figure 2B). The nature of this protein is currently unclear, but it might be similar to a 45 kDa protein previously described to be present in p85 and p110 IPs from various tissues (Pons et al., 1995).

P110a and p110 3 have been shown to interact with Ras-GTP (Kodaki et al., 1995; Rodriguez-Viciana et al., 1994 and 1996). The region required for this interaction lies between AA 133 and 314 of these PI3Ks (Rodriguez-Viciana WO 97/46688 PCT/GB97/01471 28 et al., 1996). Despite the relatively low sequence conservation with p1 and p110 O in this region (Figure 1C), certain apparently critical amino acids are conserved as p110 6 does interact with Ras in vitro, in a GTP-dependent manner (Figure 2C).

p1106 binds ras, but not rac or rho Incubation of GST-p 1108/p85a was found to retain GTP-bound wild-type ras or oncogenic V12-ras (Fig. 2C). This was not the case with GDP-loaded ras, or with A38-ras, a functionally dead ras mutant. Similar as for pll0a, no binding of rho and rac could be demonstrated (data not shown).

1 0 Lipid kinase activity of p1108 When tested in the presence of Mg 2 p110 6 was found to phosphorylate Ptdlns, PtdIns4P and PtdIns(4,5)P 2 (Fig. 3A). HPLC analysis confirmed that these lipids are phosphorylated at the D3 position (Fig. 3B). Substrate preference in vitro was Ptdlns >PtdIns4P> PtdIns(4,5)P 2 (data not shown).

1 5 Lipid kinase activity was lower in the presence of Mn 2 than in the presence of Mg 2 (tested over the concentration range of 0.25 to 16 mM; data not shown). Specific activity of p1106, isolated from Sf9 cells, was a factor lower than that of pll0a (data not shown). Taken together, these data establish p 1 106 as a genuine class I PI3K.

P1106 does not phosphorylate p85 but autophosphorylates.

The p85 subunit has been demonstrated to be a substrate for a Mn 2 dependent phosphorylation by the p10a catalytic subunit (Carpenter et al., WO 97/46688 PCT/GB97/01471 29 1993; Dhand et al., 1994). In contrast, GST-pl 10 failed to phosphorylate coexpressed p85a, p 85 p or p 8 5y under a variety of in vitro conditions (partial data shown in Fig. 4A; no activity was seen either in the presence of Mg 2 or Mn2+). p85y lacks an SH3 domain, and the absence of phosphorylation of this molecule by p110 6 argues against the possibility that an intermolecular interaction of the p85a/p SH3 domain with the p1106 proline-rich region is locking up the p85 molecules for efficient phosphorylation by p1106. In order to exclude that p1106 had already fully phosphorylated p85 during the in vivo co-expression in insect cells, exogenous purified p85a was added to immobilized GST-pll06. After washing away the excess p85, bound p85 was found to be efficiently phosphorylated by p 1 10, but again not by p1106 (data not shown). When untagged p1106, in complex with 85a or p85 P, was subjected to an in vitro kinase assay in the presence of Mn 2 p1106 autophosphorylated ((Fig. 4B 1 5 note that this activity is largely absent in immobilised GST-p 1106 (Fig. 4B)).

Such phosphorylation was not seen in p110a/p85 complexes, in which again was found to be phosphorylated (Fig. 4B). Phosphoamino acid analysis showed that the phosphorylation on p1106 occurred on serine (Fig. 4B).

Both the phosphorylation of p85 by pll0a and the autophosphorylation of p1106 were observed to be largely Mn 2 dependent, with only very weak phosphorylation in the presence of Mg 2 4 (data not shown).

Autophosphorylation of p1106 resulted in reduced lipid kinase activity.

In order to exclude the possiblity that the observed phosphorylation of p1106 was due to a coprecipitated protein kinase, a kinase-defective p1106 mutant was generated. This was done by converting arginine 894 to proline in p 1 106, generating p1106-R894P. The mutated arginine residue is located in the conserved DRX 3

NX

12 1 3 DFG motif of the kinase domain, likely to be part WO 97/46688 PCT/GB97/01471 of the catalytic loop as in protein kinases (Taylor et al., 1992, Zvelebil et al., 1996). A similar mutation in bovine pl10a (R916P) has been found to completely knock out catalytic activity (Dhand et al., 1994). As is clear from Fig. 4C, p1106-R894P, expressed in insect cells, was no longer phosphorylated in precipitates of p 1 106, indicating that the latter has indeed autophosphorylation capacity. Likewise, lipid kinase activity was found to be lost by p1108-R894P (data not shown).

We have produced polyclonal antisera to the phosphorylated form of p1106.

The C-terminal peptide sequence 1044 was phosphorylated at the serine 1 0 residue 1033 and used to immunize rabbits. The antisera directed against the phosphorylated peptide has enabled us to establish that pl106 is phosphorylated in vivo and upon cytokine stimulation this phosphorylation is enhanced (results not shown).

Drug sensitivity of p1106 catalytic activity 1 5 pll0a and 6 lipid kinase activity were found to exhibit a similar sensitivity to inhibition by wortmannin and LY294002 (Fig.5), with an IC 5 0 of 5 nM (for wortmannin) and 0.5 MM (for LY294002). Likewise, the autophosphorylation activity of p1106 was also inhibited by wortmannin in the nanomalar range (data not shown) Tissue distribution of p110 6 The expression pattern of p1106 was investigated by Northern blot analysis of polyA' RNA of human tissues, and compared with that of pllOa and p1103. A single messenger mRNA species of approximately 6 kb was found WO 97/46688 PCT/GB97/01471 31 to be particularly highly expressed in white blood cell populations i.e. spleen, thymus and especially peripheral blood leucocytes (the latter contains all white blood cells with only the majority of the erythrocytes being removed) (Fig. In some Northern blot experiments, an additional -5 kb messenger for p1108 was also observed (data not shown). Low levels of p1106 messenger RNA expression were found in most other tissues examined, although it is difficult to exclude the possibility that blood cell contamination is responsible for this p1106 mRNA signal. pll110 and pll0 were also found to be expressed in most tissues examined (Fig. 6).

Antibodies specific for p110a and 8 were then used to assay the expression of these PI3K at the protein level. Upon testing different rat tissues, a 110 kDa protein reactive with p1108 antibodies was found in spleen and thymus, but not in any of the other tissues tested (Fig. This pattern largely confirms the data of the Northern blot analysis described above. p1106 was 1 5 also found to be present in both primary and transformed white blood cells, independent of their differentiation stage (Fig. In the primary blood cells, both the lymphoid and myeloid cell populations were positive for p1106 whereas platelets were not (Fig. Both T Jurkat, HPB All) and B Raji, HFB1) cell lines expressed p1108 (Fig. The 110 kDa p1108 was not found in Rat-1, NIH 3T3 and Swiss 3T3 fibroblasts, LS174T and COLO 320HSR colon adenocarcinomas, A431 epidermoid carcinoma, ECC-1 endometrial carcinoma and HEp-2 larynx carcinoma (Fig. 7) nor in CHO chinese hamster ovary, POC small-cell lung cancer cell line, porcine and bovine aortic endothelial cells, MDA-MB-468 breast adenocarcinoma, and primary human muscle and fibroblasts (data not shown). In conclusion, it appears that p 1 108 is selectively expressed in leukocytes.

WO 97/46688 PCT/GB97/01471 32 In contrast to p1106, pllOa was found in most of the tissues and cell lines investigated, including the white blood cells (Fig. 7).

Micro Injection of Anti p110 6 Polyclonal Antibodies Into CSF-1 Stimulated Murine Macrophages The possible function of p110 6 was investigated further by a series of micro injection experiments of the murine macrophage cell-line, Bad with antisera to p1106 and pllO. Prior to micro injection, Bad cells were deprived of CSF1 for 24 hours. CSF1 deprivation primes cells to divide and become motile when subsequently exposed to CSF1. Affinity purified anti p1106 polyclonal antibodies were micro injected into CSF1 deprived Bad cells followed by exposure to CSF1 for 10-15 minutes.

The micro injected Bad cells show marked alterations in cellular morphology. The normal cell membrane ruffling disappears and cytoplasmic retraction occurs. The cytoskeleton of micro injected Bad cells was 1 5 visualised using a phalloidin-rhodamine conjugate and figure 10 shows a representative sample of such cells showing a disorganised cytoskeletal arrangement. The injection of anti p110a does not produce an equivalent effect.

Interestingly a similar phenotype is shown by expression of the dominantnegative small GTP-binding protein rac, N17RAC. This suggests that p1108 may be part of the same signalling cascade that may be involved in cytoskeletal organisation and cellular motility.

p1106 is involved in cytokine signalling WO 97/46688 PCT/GB97/01471 33 In leucocytes, p85-binding PI3Ks have been implicated in a wide variety of signalling events including signalling via cytokine and complement receptors, integrins, Fc receptors, B and T cell antigen receptors and their accessory molecules such as CD28 (reviewed by Stephens et al., 1993; Fry, 1994).

Therefore, it is clear that a multitude of signalling processes could be potentially linked to p110 6 A crucial question is whether selective coupling of p1106 to the above-mentioned signalling/receptor complexes occurs in cells that also contain other class I PI3K, given the observation that different pll0s seem to be complexed with the same'p85 isoforms (Fig. 2B). We addressed this important question in the context of cytokine signal transduction, operative in diverse types of leukocytes.

Different families of cytokines transduce signals via discrete classes of receptors that share common gpl30, P or y chains, or via receptors with intrinsic tyrosine kinase activity (reviewed in Taga and Kishimoto, 1995).

1 5 Whereas PI3K activation by cytokines signalling via gpl30 has not been reported, activation of p85-binding PI3K in response to cytokine signalling via the common p chain (eg IL3), common y chain (eg IL4), or via tyrosine kinase receptors (such as c-kit, which binds Stem Cell Factor (SCF)) has been demonstrated (Wang et al, 1992; Gold et al, 1994). We examined the ability of IL3, IL4 and SCF to couple to p1106 and pllOa in cytokine-dependent leukocyte cell lines. An identical pattern of phosphotyrosine-containing proteins, specific to the cytokine used for stimulation, was found to coprecipitate with pll0 and p1106 antibodies (Fig. 8, panel In the IL3and IL4- responsive Ba/F3 pre-B and myeloid progenitor FD-6 cell lines (Fig.

8A; data for FD-6 are not shown), IL3-treatment induced the appearance in p110a/6 IPs of an unknown protein of 100 kDa and the 70 kDa protein tyrosine phosphatase, SHP2 (Fig. 8A, panel The 170 kDa protein co- WO 97/46688 PCT/GB97/01471 34 precipitated upon IL4 stimulation (Fig. 8A, panel a) was shown by immunoblotting to be IRS-2, the major substrate of IL4-induced phosphorylation in these cells (data not shown). Fig. 8B shows the results of similar analyses in MC/9 mast cells. Following SCF stimulation, both and p1106 IPs contained an unidentified 100 kDa tyrosine-phosphorylated protein as well as a 150 kDa protein identified as c-kit, the SCF receptor (Fig. 8B, panels a and Taken together, these data indicate that and p1106 show no apparent differences in their recruitment to a variety of activated cytokine receptor complexes. In addition, the implication in cytokine signalling of at least two members of the p85-binding PI3K class reveals a previously unrecognised complication of signal transduction pathways downstream of these cytokine receptors.

Expression of PI3 Kinase p110 Sub Units in Murine and Human Melanoma Cell-Lines.

The expression of p1106 was further investigated in various murine and human melanoma cell-lines. A characteristic feature of a melanoma is the aggressive nature of the metastasis associated with this cancer. The possible involvement of p110 8 in metastasis was investigated by analysing the relative abundance of p110 6 protein in a range of murine and human cell-lines.

Western blots were used to assess the levels of p110 a and P as well as p110 6 J774, a murine cell-line, was used as a positive control for the murine western blots. Neonatal melanocytes were used as a control for the human western blot. Table 1 indicates that pll0a and P are constitutively expressed in both control and melanoma cell-lines of both murine and human origin. Interestingly, the murine control cell-line J744 shows markedly reduced levels of p110 6 when compared to the murine melanoma cell-lines.

WO 97/46688 PCT/GB97/01471 However detectable levels of p1106 are found in human neonatal melanocytes. This may be explained by the nature of these human control cells. The expression of p1106 in these control cells may be explained by the relatively recent migration of these cells in the human skin and therefore residual levels of p1108 may be present in these cells. Adult melanocytes have prolonged residence in skin and the level of p1106 may be reduced to undetectable levels commensurate with their terminal differentiation.

We have described a novel human p110 subunit, p1106, which is part of the PI3 kinase family. p1106 shows a restricted expression pattern, only accumulating to significant levels in white blood cells populations and particularly in peripheral blood leucocytes. The motile nature of these cells has lead us to propose that this member of the PI3 kinase family may be involved in regulating the motility of cells via cytoskeletal reorganisation.

The data relating to murine and human melanoma cell lines is interesting but 1 5 inconclusive with regard to human melanomas. The use of tissue biopsies of normal human melanocytes and human melanomas will allow this to be resolved.

WO 97/46688 WO 9746688PCT/GB97/01471 36 Table 1.

Expression of p110 Subunits in Murine Melanomas Cell-line ICharacteristic 6 a R eference Murmne J774 Control This study Melan-c Melanoma Melan-pi Melanoma Wilson et al 1989 Melan-a Melanoma Wilson et al 1989 Tu-2d Mel-ab Melanoma Dooley et al 1988 Mel-ab-LTR- Melanoma Dooley et al 1988 Ras2 Mel-ab-LTR Melanoma Dooley et al 1988 Ras 3 Mel-ab-pMT Melanoma Dooley et al 1988 B16 F1 Melanoma Fidler et al 1975 (weakly metastatic) B16 F10 Melanoma Fidler et. al 1975 (highly metastatic) WO 97/46688 WO 9746688PCT/GB97/01471 37 Table 1 Continued Expression of p110 Subunits in Human Melanomas Cell-line JCharacteristic 8 a P Reference Human A375P Melanoma Easty et al 1995 (weakly metastatic) A375M Melanoma Easty et al 1995 (highly metastatic) WM164 Melanoma Easty etall1995 WM451 Melanoma Easty et al 1995 DX3 Melanoma Ormerod et al 1986 (weakly metastatic) DX3-LT5.1 Melanoma Ormerod et al 1986 (Highly metastatic) Control Primary cells This study (human neonatal melanocytes) WO 97/46688 PCT/GB97/01471 38 References Antonetti, Algenstaedt, P. and Kahn, C.R. (1996) Insulin receptor substrate 1 binds two novel splice variants of the regulatory subunit of phosphatidylinositol 3- kinase in muscle and brain. Mol. Cell. Biol., 16, 2195- 2203.

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SUBSTITUTE SHEET (RULE 26)

Claims (29)

1. An isolated autophosphorylating polypeptide, or fragment thereof, possessing P13 kinase activity represented by the amino acid sequence shown in Figure 1, or a homologue thereof, optionally modified by deletion, substitution or addition of at least one amino acid residue and wherein said polypeptide is selectively expressed in white blood cells and/or melanomas.

2. An isolated polypeptide according to claim 1 wherein said polypeptide is capable of association with at least one mammalian p85 adaptor polypeptide.

3. An isolated polypeptide according to any one of claims 1 and 2 wherein said S. polypeptide is characterised by a domain having a proline content between 35-45%.

4. An isolated polypeptide according to claim 3 wherein said proline rich domain is S. ideally at position 292-311 of the protein sequence data shown in Figure 1 but may be at a homologous site in an equivalent P13 kinase. 15

5. An isolated polypeptide according to any one of claims 1-4 wherein said polypeptide is of mammalian origin and ideally human.

6. An isolated nucleic acid molecule that encodes the polypeptide according to any one of claims

7. An isolated nucleic acid molecule according to claim 6 wherein the nucleic acid sequence is either cDNA or genomic DNA.

8. An isolated nucleic acid molecule according to claim 6 or 7 wherein said molecule is in a cloned recombinant vector. 48

9. An isolated nucleic acid molecule according to any one of claims 6-8 wherein said molecule, or part thereof, is adapted for the recombinant expression of the polypeptide according to any one of claims

10. A host cell, transfected or transformed using the construct of the invention according to claim 8 or 9 wherein said construct directs the recombinant synthesis of a whole or a part of the polypeptide according to any one of claims

11. A host cell line according to claim 8 wherein said cell line is an insect cell line.

12. The use of the recombinantly expressed polypeptide according to claim 8 or 9 or the isolated polypeptide according to any one of claims 1-5 for the production of antibodies to o: pllOa. S

13. An antibody, or part thereof, according to claim 12 wherein said antibody is monoclonal.

14. A method for the identification of the tissue specific expression of the polypeptide *o*o according to any one of claims 1-5 including determining the presence of either, or both, the relevant polypeptide and/or the mRNA and/or cDNA encoding same.

15. A method according to claim 14 wherein said method includes binding at least two nucleic acid molecule primers adapted to hybridise to at least one selected part of the nucleic acid molecule of the invention to the said cDNA.

16. A method according to claim 14 or 15 wherein said method includes providing the conditions for amplifying and purifying at least one part of said nucleic acid molecule according to any one of claims 6-11 using said primers. 49

17. A method according to claim 14 wherein said method includes using an antibody according to claim 12 or 13 for the detection of said polypeptide wherein said use involves either ELISA, western blot, immunoprecipitation or immunofluorescence.

18. A method for identifying agents effective at modulating the kinase activity of the polypeptide, according to any one of claims 1-5, including exposing the polypeptide, either in vitro or in vivo, to agents that may have modulating effects and then observing the kinase activity of said polypeptide.

19. A method according to claim 18 wherein potentially antagonistic agents are screened using computer aided modelling or conventional laboratory techniques.

20. A method according to claim 18 or 19 wherein cells, expressing the polypeptide according to any one of claims 1-5, are exposed to potential antagonists and the motility of S* said cells is monitored.

21. A pharmaceutical/veterinary composition including an agent effective at modulating the activity of the polypeptide according to any one of claims

22. A pharmaceutical/veterinary composition according to claim 21 which optionally also includes a diluant, carrier or excipient and/or is in unit dosage form.

23. A method for controlling the motility of cells including exposing a population of cells to either the polypeptide according to any one of claims 1-4, or an antagonist or an agonist thereof.

24. A method according to claim 23 wherein the motility of cells is enhanced by exposure of the cells to the polypeptide of the invention.

Use of an agent effective at blocking the activity of the polypeptide according to any one of claims 1-5 for controlling cell motility.

26. Use of the polypeptide according to any one of claims 1-5 for enhancing cell motility.

27. Antisense oligonucleotide adapted to hybridize to the nucleic acid of claims 6-9.

28. Antisense oligonucleotide according to claim 27 wherein said oligonucleotide is modified as hereindescribed.

29. A pharmaceutical/veterinary composition comprising the antisense oligonucleotide of claim 27 or 28. Dated this 6th day of March 2000 ."C PATENT ATTORNEY SERVICES 10 Attorneys for S LUDWIG INSTITUTE FOR CANCER RESEARCH 0 e C